Now, you would have to have gotten hold of Chrono Trigger the instant it was released and be somehow cut off from all information about the game (since information on important plot events was already known to many gamers before it was released) to play the game truly organically. But if you did, the game elaborately leads you to believe that Magus, Jackass Dark Wizard and Evil Overlord Extraordinaire of A.D. 600, is the Big Bad, that your mission to save the world will successfully conclude if you can get to Magus and kill him dead before he can create Lavos, the Planet Eater that will destroy life 1,400 years later. Because Magus is a dick. He really is. He slaughtered countless Guardia soldiers and civilians, and he turned Frog into a frog just for the lolz (no, really; he stated himself he did it just for fun).
So you spend a good half of the game running all over time collecting the various MacGuffins you need to gain access to Magus's Evil Castle of Supreme Darkness--no, it really is dark and evil and makes you want to run home to Mommy--and then when you finally get there, it proves to be as wicked and grueling as any Very Definitely Final Dungeon you'd care to name. Probably never has a dungeon's theme been so well executed; by the time you finally whack First Lieutenant Ozzie and gain access to Magus's shrine, the tension is so palpable you're a zombie if your heart isn't racing.
After you heal up and save up, you walk down a very long, dark stairway while ominous chanting grows slowly louder and you get slowly stalked by bats that, unless you sprint down the stairs, you have to kill. Then you walk into Magus's chamber in total silence and total darkness, and with each step forward you take eerie blue-purple flames erupt on both sides of you while Magus chants.
Neuga, ziena, zieber, zom...
Now the chosen time has come...
Exchange this world for--!
That, friends, is a summoning ritual. Which we sure as hell are here to interrupt.
And when it shortly comes down to throw down for the fate of the world and Frog's amphibian honor, the Black Wind will embrace you with this music while you battle the Jackass Wizard. Which isn't easy. But listen to this music; did you think it would be easy?
Magus's theme music, like all good character theme music, fits him. Dark, threatening, dangerous, evil... even a little taunting. Like Magus, the music calls to you: "Give me your best shot... if you're prepared for the void!"
Then you finally whip the bastard and it turns out the game's only half over and Magus didn't create Lavos. He just summoned Lavos. Because he wanted to kick Lavos's ass. Which incidentally aligns with your goals. You can only imagine the awesome insanity that ensues.
So Magus wasn't the final battle of Chrono Trigger, but if you were completely uninitiate, the storyline would very much convince you he was. And he has the heart-pumping battle music to back it up.